My student is attempting the Blasting Flu Viruses project. When completing the example we do not see any regions of the protein in lower case letters indicating a change. I do see a + sign and empty space when comparing the sequences but no lower case letters. Are we doing something incorrectly?

This is a great project especially since everyone gets the flu shot every year. It sounds like you are doing your BLAST searches correctly. The blank spaces represent spots where the two protein sequences are very different and this difference could result in a phenotypic change. An example would be going from lysine to aspartic acid (positive charge to a negative charge). The + sign indicates places where the two protein sequences differ but the amino acids are similar so the difference may not result in a phenotypic change. An example would be going from leucine to valine (both uncharged, hydrophobic).

As far as identifying regions that are most likely to change, you can hypothesize that regions that contain mismatches are more likely to change. This is a strong hypothesis because changes in these regions have been identified in different viruses that were able to infect and replicate in the host. That is why these different versions of HA are present in the NCBI databases.